ENH: Fix rescale and invert intensity for ITKv4 ANTS

ContinuousRegistration/Source/datasets.py

@@ -427,6 +427,7 @@ class DIRLAB(Dataset):
                 )
             else:
                 # If no mask was provided, just generate mask filled with ones
+                logging.warning('Masks not found for DIRLAB. Creating mask with elements set to one.')
                 mask_file_names = [
                     create_mask_by_size(image_file_names[i],
                                         os.path.join(output_directory, 'tmp', 'masks',
@@ -717,6 +718,7 @@ class POPI(Dataset):
                                    os.path.join(mask_directory, sub_directory, 'mhd', '50.mhd'))
             else:
                 # If no mask was provided, just generate mask filled with ones
+                logging.warning('Masks not found for POPI. Creating mask with elements set to one.')
                 mask_file_names = [
                     create_mask_by_size(image_file_names[i],
                                         os.path.join(output_directory, 'tmp', 'masks',

ContinuousRegistration/Source/metrics.py

@@ -39,8 +39,14 @@ def hausdorff(superelastix, point_sets, deformation_field_file_names):
 
 def inverse_consistency(superelastix, displacement_field_file_names, mask_file_names):
     try:
-        composed_0 = sitk.GetArrayFromImage(sitk.ReadImage(compose_displacement_fields(superelastix, displacement_field_file_names[0], displacement_field_file_names[1])))
-        composed_1 = sitk.GetArrayFromImage(sitk.ReadImage(compose_displacement_fields(superelastix, displacement_field_file_names[1], displacement_field_file_names[0])))
+        composed_0 = sitk.GetArrayFromImage(
+            sitk.ReadImage(
+                compose_displacement_fields(
+                    superelastix, displacement_field_file_names[0], displacement_field_file_names[1])))
+        composed_1 = sitk.GetArrayFromImage(
+            sitk.ReadImage(
+                compose_displacement_fields(
+                    superelastix, displacement_field_file_names[1], displacement_field_file_names[0])))
     except Exception:
         return (
             {'3. InverseConsistency': np.NaN},
@@ -48,18 +54,14 @@ def inverse_consistency(superelastix, displacement_field_file_names, mask_file_n
         )
 
     mask_0 = sitk.GetArrayFromImage(sitk.ReadImage(mask_file_names[0])) > 0
-    norm_0 = np.linalg.norm(composed_0, axis=-1)
-    norm_0 = norm_0[mask_0]
-    norm_0 = np.ma.array(norm_0, mask=np.isnan(norm_0))
+    norm_0 = np.linalg.norm(composed_0[mask_0], axis=-1).flatten()
 
     mask_1 = sitk.GetArrayFromImage(sitk.ReadImage(mask_file_names[1])) > 0
-    norm_1 = np.linalg.norm(composed_1, axis=-1)
-    norm_1 = norm_1[mask_1]
-    norm_1 = np.ma.array(norm_1, mask=np.isnan(norm_1))
+    norm_1 = np.linalg.norm(composed_1[mask_1], axis=-1).flatten()
 
     return (
-        {'3. InverseConsistency': np.mean(norm_0)},
-        {'3. InverseConsistency': np.mean(norm_1)}
+        {'3. InverseConsistency': float(np.nanmean(norm_0))},
+        {'3. InverseConsistency': float(np.nanmean(norm_1))}
     )
 
 

ContinuousRegistration/Submissions/TeamElastix/ITKv4_SVF_ANTS_CC_Brains.json

+{
+  "Datasets": [
+    "LPBA40",
+    "IBSR18",
+    "CUMC12",
+    "MGH10",
+    "HAMMERS"
+  ],
+  "Components": [
+    {
+      "Name": "MultiStageTransformController",
+      "NameOfClass": "NiftyregItkMultiStageComponent",
+      "ExecutionOrder": [ "RegistrationMethod1", "RegistrationMethod2" ],
+      "Dimensionality": "3",
+      "PixelType": "double"
+    },
+    {
+      "Name": "RegistrationMethod1",
+      "NameOfClass": "NiftyregAladinComponent",
+      "MaximumNumberOfIterations": "1"
+    },
+    {
+      "Name": "RegistrationMethod2",
+      "NameOfClass": "ItkImageRegistrationMethodv4Component",
+      "InternalComputationValueType": "double",
+      "Dimensionality": "3",
+      "PixelType": "float",
+      "NumberOfLevels": "3",
+      "ShrinkFactorsPerLevel": [ "8", "4", "2" ],
+      "SmoothingSigmasPerLevel": [ "4", "2", "1" ],
+      "RescaleIntensity": ["0", "1"]
+    },
+    {
+      "Name": "TransformResolutionAdaptor",
+      "NameOfClass": "ItkGaussianExponentialDiffeomorphicTransformParametersAdaptorsContainerComponent",
+      "ShrinkFactorsPerLevel": [ "8", "4", "2" ],
+      "Dimensionality": "3"
+    },
+    {
+      "Name": "FixedImage",
+      "NameOfClass": "ItkToNiftiImageHybridSourceComponent",
+      "Dimensionality": "3",
+      "PixelType": "float"
+    },
+    {
+      "Name": "MovingImage",
+      "NameOfClass": "ItkToNiftiImageHybridSourceComponent",
+      "Dimensionality": "3",
+      "PixelType": "float"
+    },
+    {
+      "Name": "FixedMask",
+      "NameOfClass": "ItkToNiftiImageHybridSourceComponent",
+      "PixelType": "unsigned char",
+      "Dimensionality": "3"
+    },
+    {
+      "Name": "MovingMask",
+      "NameOfClass": "ItkToNiftiImageHybridSourceComponent",
+      "PixelType": "unsigned char",
+      "Dimensionality": "3"
+    },
+    {
+      "Name": "Metric2",
+      "NameOfClass": "ItkANTSNeighborhoodCorrelationImageToImageMetricv4Component",
+      "Dimensionality": "3",
+      "PixelType": "float"
+    },
+    {
+      "Name": "Transform2",
+      "NameOfClass": "ItkGaussianExponentialDiffeomorphicTransformComponent",
+      "GaussianSmoothingVarianceForTheUpdateField": "2.0",
+      "GaussianSmoothingVarianceForTheConstantVelocityField": "1.0"
+    },
+    {
+      "Name": "Optimizer2",
+      "NameOfClass": "ItkGradientDescentOptimizerv4Component",
+      "InternalComputationValueType": "double",
+      "MaximumNumberOfIterations": "8",
+      "MaximumStepSizeInPhysicalUnits": "1.0",
+      "LearningRate": "0.25",
+      "EstimateScales": "True",
+      "EstimateLearningRate": "False"
+    },
+    {
+      "Name": "DisplacementField",
+      "NameOfClass": "ItkDisplacementFieldSinkComponent",
+      "Dimensionality": "3",
+      "PixelType": "float"
+    },
+    {
+      "Name": "TransformToDisplacementField",
+      "NameOfClass": "ItkTransformDisplacementFilterComponent",
+      "Dimensionality": "3",
+      "PixelType": "float"
+    }
+  ],
+  "Connections": [
+    {
+      "Out": "TransformResolutionAdaptor",
+      "In": "RegistrationMethod2"
+    },
+    {
+      "Out": "FixedImage",
+      "In": "TransformResolutionAdaptor",
+      "NameOfInterface": "itkImageDomainFixedInterface"
+    },
+    {
+      "Out": "FixedImage",
+      "In": "RegistrationMethod1",
+      "NameOfInterface": "NiftyregReferenceImageInterface"
+    },
+    {
+      "Out": "MovingImage",
+      "In": "RegistrationMethod1",
+      "NameOfInterface": "NiftyregFloatingImageInterface"
+    },
+    {
+      "Out": "FixedMask",
+      "In": "RegistrationMethod1",
+      "NameOfInterface": "NiftyregInputMaskInterface"
+    },
+    {
+      "Out": "FixedImage",
+      "In": "RegistrationMethod2",
+      "NameOfInterface": "itkImageFixedInterface"
+    },
+    {
+      "Out": "MovingImage",
+      "In": "RegistrationMethod2",
+      "NameOfInterface": "itkImageMovingInterface"
+    },
+    {
+      "Out": "Metric2",
+      "In": "RegistrationMethod2"
+    },
+    {
+      "Out": "Transform2",
+      "In": "RegistrationMethod2"
+    },
+    {
+      "Out": "Optimizer2",
+      "In": "RegistrationMethod2"
+    },
+    {
+      "Out": "FixedImage",
+      "In": "Transform2"
+    },
+    {
+      "Out": "RegistrationMethod1",
+      "In": "MultiStageTransformController"
+    },
+    {
+      "Out": "RegistrationMethod2",
+      "In": "MultiStageTransformController"
+    },
+    {
+      "Out": "MultiStageTransformController",
+      "In": "TransformToDisplacementField"
+    },
+    {
+      "Out": "FixedImage",
+      "In": "TransformToDisplacementField",
+      "NameOfInterface": "itkImageDomainFixedInterface"
+    },
+    {
+      "Out": "TransformToDisplacementField",
+      "In": "DisplacementField"
+    },
+    {
+      "Out": "FixedMask",
+      "In": "Metric2"
+    },
+    {
+      "Out": "FixedMask",
+      "In": "RegistrationMethod1",
+      "NameOfInterface": "NiftyregInputMaskInterface"
+    }
+  ]
+}

ContinuousRegistration/Submissions/TeamElastix/ITKv4_SVF_ANTS_CC.json → ContinuousRegistration/Submissions/TeamElastix/ITKv4_SVF_ANTS_CC_Lungs.json

 {
-    "Datasets": ["POPI", "DIRLAB", "EMPIRE", "LPBA40", "IBSR18", "CUMC12", "MGH10", "SPREAD", "HAMMERS"],
+    "Datasets": ["POPI", "DIRLAB", "EMPIRE", "SPREAD" ],
     "Components": [
         {
             "Name": "RegistrationMethod",
             "NameOfClass": "ItkImageRegistrationMethodv4Component",
             "NumberOfLevels":  "4" ,
-            "ShrinkFactorsPerLevel": [ "16", "8", "4", "2" ],
+            "ShrinkFactorsPerLevel": [ "12", "8", "4", "2" ],
             "SmoothingSigmasPerLevel": [ "8", "4", "2", "1" ],
             "Dimensionality": "3",
             "RescaleIntensity": ["0", "1"],
-            "InvertIntensity": "True",
-            "MetricSamplingPercentage": "0.2",
-            "MetricSamplingStrategy": "Random"
+            "InvertIntensity": ["True"]
         },
         {
             "Name": "FixedImageCropper",
@@ -62,7 +60,7 @@
         {
             "Name": "Optimizer",
             "NameOfClass": "ItkGradientDescentOptimizerv4Component",
-            "NumberOfIterations": "48",
+            "NumberOfIterations": "8",
             "LearningRate": "0.25",
             "EstimateScales": "True",
             "EstimateLearningRate": "False"
@@ -72,13 +70,13 @@
             "NameOfClass": "ItkGaussianExponentialDiffeomorphicTransformComponent",
             "InternalComputationValueType": "double",
             "Dimensionality": "3",
-            "GaussianSmoothingVarianceForTheConstantVelocityField": "1.0",
-            "GaussianSmoothingVarianceForTheUpdateField": "2.0"
+            "GaussianSmoothingVarianceForTheUpdateField": "3.0",
+            "GaussianSmoothingVarianceForTheConstantVelocityField": "0.5"
         },
         {
             "Name": "TransformResolutionAdaptor",
             "NameOfClass": "ItkGaussianExponentialDiffeomorphicTransformParametersAdaptorsContainerComponent",
-            "ShrinkFactorsPerLevel": [ "16", "8", "4", "2" ],
+            "ShrinkFactorsPerLevel": [ "12", "8", "4", "2" ],
             "Dimensionality": "3"
         },
         {
@@ -165,10 +163,6 @@
         {
             "Out": "FixedMask",
             "In": "Metric"
-        },
-        {
-            "Out": "MovingMask",
-            "In": "Metric"
         }
     ]
 }

ContinuousRegistration/Submissions/TeamElastix/NiftyRegAffineITKANTSHybridBrains.json

+{
+  "Datasets": [
+    "LPBA40",
+    "IBSR18",
+    "CUMC12",
+    "MGH10",
+    "HAMMERS"
+  ],
+  "Components": [
+    {
+      "Name": "MultiStageTransformController",
+      "NameOfClass": "NiftyregItkMultiStageComponent",
+      "ExecutionOrder": [ "RegistrationMethod1", "RegistrationMethod2" ],
+      "Dimensionality": "3",
+      "PixelType": "double"
+    },
+    {
+      "Name": "RegistrationMethod1",
+      "NameOfClass": "NiftyregAladinComponent",
+      "MaximumNumberOfIterations": "1"
+    },
+    {
+      "Name": "RegistrationMethod2",
+      "NameOfClass": "ItkImageRegistrationMethodv4Component",
+      "InternalComputationValueType": "double",
+      "Dimensionality": "3",
+      "PixelType": "float",
+      "NumberOfLevels": "3",
+      "ShrinkFactorsPerLevel": [ "8", "4", "2" ],
+      "SmoothingSigmasPerLevel": [ "4", "2", "1" ],
+      "RescaleIntensity": ["0", "1"]
+    },
+    {
+      "Name": "TransformResolutionAdaptor",
+      "NameOfClass": "ItkGaussianExponentialDiffeomorphicTransformParametersAdaptorsContainerComponent",
+      "ShrinkFactorsPerLevel": [ "8", "4", "2" ],
+      "Dimensionality": "3"
+    },
+    {
+      "Name": "FixedImage",
+      "NameOfClass": "ItkToNiftiImageHybridSourceComponent",
+      "Dimensionality": "3",
+      "PixelType": "float"
+    },
+    {
+      "Name": "MovingImage",
+      "NameOfClass": "ItkToNiftiImageHybridSourceComponent",
+      "Dimensionality": "3",
+      "PixelType": "float"
+    },
+    {
+      "Name": "FixedMask",
+      "NameOfClass": "ItkToNiftiImageHybridSourceComponent",
+      "PixelType": "unsigned char",
+      "Dimensionality": "3"
+    },
+    {
+      "Name": "MovingMask",
+      "NameOfClass": "ItkToNiftiImageHybridSourceComponent",
+      "PixelType": "unsigned char",
+      "Dimensionality": "3"
+    },
+    {
+      "Name": "Metric2",
+      "NameOfClass": "ItkANTSNeighborhoodCorrelationImageToImageMetricv4Component",
+      "Dimensionality": "3",
+      "PixelType": "float"
+    },
+    {
+      "Name": "Transform2",
+      "NameOfClass": "ItkGaussianExponentialDiffeomorphicTransformComponent",
+      "GaussianSmoothingVarianceForTheUpdateField": "2.0",
+      "GaussianSmoothingVarianceForTheConstantVelocityField": "1.0"
+    },
+    {
+      "Name": "Optimizer2",
+      "NameOfClass": "ItkGradientDescentOptimizerv4Component",
+      "InternalComputationValueType": "double",
+      "MaximumNumberOfIterations": "8",
+      "MaximumStepSizeInPhysicalUnits": "1.0",
+      "LearningRate": "0.25",
+      "EstimateScales": "True",
+      "EstimateLearningRate": "False"
+    },
+    {
+      "Name": "DisplacementField",
+      "NameOfClass": "ItkDisplacementFieldSinkComponent",
+      "Dimensionality": "3",
+      "PixelType": "float"
+    },
+    {
+      "Name": "TransformToDisplacementField",
+      "NameOfClass": "ItkTransformDisplacementFilterComponent",
+      "Dimensionality": "3",
+      "PixelType": "float"
+    }
+  ],
+  "Connections": [
+    {
+      "Out": "TransformResolutionAdaptor",
+      "In": "RegistrationMethod2"
+    },
+    {
+      "Out": "FixedImage",
+      "In": "TransformResolutionAdaptor",
+      "NameOfInterface": "itkImageDomainFixedInterface"
+    },
+    {
+      "Out": "FixedImage",
+      "In": "RegistrationMethod1",
+      "NameOfInterface": "NiftyregReferenceImageInterface"
+    },
+    {
+      "Out": "MovingImage",
+      "In": "RegistrationMethod1",
+      "NameOfInterface": "NiftyregFloatingImageInterface"
+    },
+    {
+      "Out": "FixedMask",
+      "In": "RegistrationMethod1",
+      "NameOfInterface": "NiftyregInputMaskInterface"
+    },
+    {
+      "Out": "FixedImage",
+      "In": "RegistrationMethod2",
+      "NameOfInterface": "itkImageFixedInterface"
+    },
+    {
+      "Out": "MovingImage",
+      "In": "RegistrationMethod2",
+      "NameOfInterface": "itkImageMovingInterface"
+    },
+    {
+      "Out": "Metric2",
+      "In": "RegistrationMethod2"
+    },
+    {
+      "Out": "Transform2",
+      "In": "RegistrationMethod2"
+    },
+    {
+      "Out": "Optimizer2",
+      "In": "RegistrationMethod2"
+    },
+    {
+      "Out": "FixedImage",
+      "In": "Transform2"
+    },
+    {
+      "Out": "RegistrationMethod1",
+      "In": "MultiStageTransformController"
+    },
+    {
+      "Out": "RegistrationMethod2",
+      "In": "MultiStageTransformController"
+    },
+    {
+      "Out": "MultiStageTransformController",
+      "In": "TransformToDisplacementField"
+    },
+    {
+      "Out": "FixedImage",
+      "In": "TransformToDisplacementField",
+      "NameOfInterface": "itkImageDomainFixedInterface"
+    },
+    {
+      "Out": "TransformToDisplacementField",
+      "In": "DisplacementField"
+    },
+    {
+      "Out": "FixedMask",
+      "In": "Metric2"
+    },
+    {
+      "Out": "FixedMask",
+      "In": "RegistrationMethod1",
+      "NameOfInterface": "NiftyregInputMaskInterface"
+    }
+  ]
+}

ContinuousRegistration/Submissions/TeamElastix/NiftyRegAffineITKANTSHybrid.json → ContinuousRegistration/Submissions/TeamElastix/NiftyRegAffineITKANTSHybridLungs.json

@@ -3,12 +3,7 @@
         "POPI",
         "DIRLAB",
         "EMPIRE",
-        "LPBA40",
-        "IBSR18",
-        "CUMC12",
-        "MGH10",
-        "SPREAD",
-        "HAMMERS"
+        "SPREAD"
     ],
     "Components": [
         {
@@ -21,7 +16,7 @@
         {
             "Name": "RegistrationMethod1",
             "NameOfClass": "NiftyregAladinComponent",
-            "MaximumNumberOfIterations": "16"
+            "MaximumNumberOfIterations": "1"
         },
         {
             "Name": "RegistrationMethod2",
@@ -29,18 +24,16 @@
             "InternalComputationValueType": "double",
             "Dimensionality": "3",
             "PixelType": "float",
-            "NumberOfLevels": "4",
-            "ShrinkFactorsPerLevel": [ "16", "8", "4", "2" ],
-            "SmoothingSigmasPerLevel": [ "8", "4", "2", "1" ],
+            "NumberOfLevels": "3",
+            "ShrinkFactorsPerLevel": [ "8", "4", "2" ],
+            "SmoothingSigmasPerLevel": [ "4", "2", "1" ],
             "RescaleIntensity": ["0", "1"],
-            "InvertIntensity": "True",
-            "MetricSamplingPercentage": "0.2",
-            "MetricSamplingStrategy": "Random"
+            "InvertIntensity": "True"
         },
         {
             "Name": "TransformResolutionAdaptor",
             "NameOfClass": "ItkGaussianExponentialDiffeomorphicTransformParametersAdaptorsContainerComponent",
-            "ShrinkFactorsPerLevel": [ "16", "8", "4", "2" ],
+            "ShrinkFactorsPerLevel": [ "8", "4", "2" ],
             "Dimensionality": "3"
         },
         {
@@ -67,20 +60,6 @@
             "PixelType": "unsigned char",
             "Dimensionality": "3"
         },
-        {
-            "Name": "FixedImageCropper",
-            "NameOfClass": "ItkCropperComponent",
-            "Dimensionality": "3",
-            "PixelType": "float",
-            "Pad": 8
-        },
-        {
-            "Name": "MovingImageCropper",
-            "NameOfClass": "ItkCropperComponent",
-            "Dimensionality": "3",
-            "PixelType": "float",
-            "Pad": 8
-        },
         {
             "Name": "Metric2",
             "NameOfClass": "ItkANTSNeighborhoodCorrelationImageToImageMetricv4Component",
@@ -97,7 +76,7 @@
             "Name": "Optimizer2",
             "NameOfClass": "ItkGradientDescentOptimizerv4Component",
             "InternalComputationValueType": "double",
-            "MaximumNumberOfIterations": "16",
+            "MaximumNumberOfIterations": "8",
             "MaximumStepSizeInPhysicalUnits": "1.0",
             "LearningRate": "0.25",
             "EstimateScales": "True",
@@ -123,30 +102,6 @@
         },
         {
             "Out": "FixedImage",
-            "In": "FixedImageCropper",
-            "NameOfInterface": "itkImageInterface"
-        },
-        {
-            "Out": "FixedMask",
-            "In": "FixedImageCropper",
-            "NameOfInterface": "itkImageFixedMaskInterface"
-        },
-        {
-            "Out": "FixedImageCropper",
-            "In": "RegistrationMethod",
-            "NameOfInterface": "itkImageFixedInterface"
-        },
-        {
-            "Out": "MovingImage",
-            "In": "MovingImageCropper",
-            "NameOfInterface": "itkImageInterface"
-        },{
-            "Out": "MovingMask",
-            "In": "MovingImageCropper",
-            "NameOfInterface": "itkImageMovingMaskInterface"
-        },
-        {
-            "Out": "FixedImageCropper",
             "In": "TransformResolutionAdaptor",
             "NameOfInterface": "itkImageDomainFixedInterface"
         },
@@ -161,12 +116,17 @@
             "NameOfInterface": "NiftyregFloatingImageInterface"
         },
         {
-            "Out": "FixedImageCropper",
+            "Out": "FixedMask",
+            "In": "RegistrationMethod1",
+            "NameOfInterface": "NiftyregInputMaskInterface"
+        },
+        {
+            "Out": "FixedImage",
             "In": "RegistrationMethod2",
             "NameOfInterface": "itkImageFixedInterface"
         },
         {
-            "Out": "MovingImageCropper",
+            "Out": "MovingImage",
             "In": "RegistrationMethod2"